DEPDC5 p.Val466=
c.1398G>C · rs1602054069 · VCV1566785
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
familial focal epilepsy with variable foci
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>A here scores Δ0.22 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.16 | GERP 3.1, phastCons 0.83 |
| Overall | ||
| CADD | 4.916 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- DEPDC5
- Protein
- p.Val466=
- Coding
- c.1398G>C
- MANE Select
- NM_001242896
- dbSNP
- rs1602054069
- Type
- single nucleotide variant
- Location
- chr22:31810594 (GRCh38)
- Gene constraint
- LOEUF 0.403 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 65.22 · 11 PDB
- Residue 466
- a turn
Disease context
familial focal epilepsy with variable foci — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Familial focal epilepsy with variable foci (Orphanet):
- Inheritance
- Autosomal dominant
- Onset
- Adolescent, Adult, Childhood, Infancy
Similar variants
- DEPDC5 p.Val466fs Pathogenic ★ same residue
- DEPDC5 c.1218-1G>A Pathogenic ★★ same condition
- DEPDC5 c.1287+1G>A Pathogenic/Likely pathogenic ★★ same condition
- DEPDC5 c.1324+1G>A Likely pathogenic ★★ same condition
- DEPDC5 c.1324+1G>T Likely pathogenic ★★ same condition
- DEPDC5 c.193+1G>T Pathogenic/Likely pathogenic ★★ same condition
- DEPDC5 c.2105-1G>A Likely pathogenic ★★ same condition
- DEPDC5 c.2634-2A>G Likely pathogenic ★★ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/depdc5-p-val466 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown